Contacts of the helix formed by residues 602 - 625 (chain B) in PDB entry 3A8P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 602 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B HIS* 3.3 19.3 + - - -
600B ALA* 3.3 4.1 + - - +
601B THR* 1.3 85.6 + - - +
603B GLN* 1.3 59.7 + - - +
604B THR* 3.6 7.8 + - - -
605B ASP* 3.1 22.2 + - - +
606B LEU* 2.9 27.2 + - - +
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Residues in contact with GLN 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ALA* 4.0 32.1 - - + +
584B HIS* 3.2 20.6 + - + +
602B SER* 1.3 70.7 - - - +
604B THR* 1.3 66.0 + - - +
606B LEU* 3.4 21.9 + - - +
607B GLU* 2.9 67.5 + - - +
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Residues in contact with THR 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B SER* 3.2 8.1 + - - -
603B GLN* 1.3 76.6 - - - +
605B ASP* 1.3 65.9 + - - +
607B GLU* 3.1 17.1 + - + +
608B ASN* 2.9 39.6 + - - +
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Residues in contact with ASP 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LYS* 3.8 11.1 + - - -
510B TRP 4.5 1.6 - - - +
511B LEU* 4.3 1.9 - - - +
600B ALA* 3.4 9.2 - - + +
601B THR* 3.2 36.3 + - - +
602B SER* 3.1 24.9 + - - +
604B THR* 1.3 78.6 - - - +
606B LEU* 1.3 62.8 + - - +
608B ASN* 3.1 9.3 + - - +
609B TRP* 3.0 47.3 + - - -
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B SER* 4.0 21.3 - - - -
584B HIS* 3.6 22.7 - - - +
585B VAL 3.6 26.7 - - - +
586B PHE* 4.0 16.3 - - + -
600B ALA* 3.4 14.3 - - + +
602B SER 2.9 17.6 + - - +
603B GLN* 3.6 25.1 - - - +
604B THR 3.3 0.2 - - - -
605B ASP* 1.3 75.9 - - - +
607B GLU* 1.3 64.7 + - + +
609B TRP* 3.3 3.3 + - - +
610B VAL* 3.0 46.0 + - + +
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Residues in contact with GLU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLN* 2.9 44.7 + - - +
604B THR* 3.1 17.5 + - + +
606B LEU* 1.3 84.2 - - + +
608B ASN* 1.3 60.2 + - - +
610B VAL* 3.4 5.1 + - - +
611B THR* 2.9 35.4 + - - +
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Residues in contact with ASN 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LYS* 3.2 25.9 + - + +
604B THR* 2.9 38.5 + - - +
605B ASP* 3.1 8.0 + - - +
607B GLU* 1.3 77.9 - - - +
609B TRP* 1.3 58.7 + - - +
611B THR* 3.8 5.1 - - - -
612B ALA* 2.9 30.5 + - - +
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Residues in contact with TRP 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LYS* 3.2 44.7 - - + +
508B ALA 3.9 3.1 - - - -
509B GLY* 3.8 25.9 - - - -
510B TRP 5.1 0.4 + - - -
511B LEU* 3.5 44.5 - - + +
538B VAL* 3.7 22.7 - - + -
540B LEU* 4.2 9.4 - - + -
545B LEU* 3.9 22.0 - - + -
586B PHE* 3.8 20.9 - + + -
600B ALA* 4.8 0.2 - - + -
605B ASP* 3.0 33.5 + - - -
606B LEU 3.6 7.2 - - - +
608B ASN* 1.3 75.7 - - - +
610B VAL* 1.3 60.6 + - - +
612B ALA* 3.6 1.7 - - + +
613B ILE* 2.9 49.6 + - + +
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Residues in contact with VAL 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B VAL* 3.9 31.6 - - + +
575B SER* 5.2 4.5 - - - +
586B PHE* 4.7 6.7 - - + -
606B LEU* 3.0 39.4 + - + +
607B GLU* 3.7 6.3 - - - +
609B TRP* 1.3 75.9 - - - +
611B THR* 1.3 65.4 + - - +
613B ILE* 4.0 1.2 - - - +
614B HIS* 3.0 50.6 + - + +
698B SER* 4.3 3.6 - - - +
704B LEU* 4.6 16.2 - - + -
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Residues in contact with THR 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B GLU* 2.9 20.4 + - - +
608B ASN* 3.8 6.5 - - - +
610B VAL* 1.3 76.7 - - - +
612B ALA* 1.3 57.1 + - - +
614B HIS* 3.9 0.9 - - - +
615B SER* 2.5 42.1 + - - +
698B SER* 3.5 37.4 + - - +
704B LEU* 6.2 0.3 - - - +
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ARG* 3.2 22.5 - - + +
507B LYS* 3.9 20.4 - - + -
540B LEU* 3.5 19.2 - - + +
608B ASN 2.9 20.6 + - - +
609B TRP* 3.6 6.1 - - + +
611B THR* 1.3 79.1 - - - +
613B ILE* 1.3 57.7 + - - +
615B SER* 3.4 1.6 + - - -
616B ALA 3.0 22.7 + - - -
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Residues in contact with ILE 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B LEU* 4.0 18.8 - - + -
545B LEU* 4.6 13.2 - - + -
568B ALA* 4.4 7.4 - - + -
571B SER* 4.7 1.8 - - - -
573B VAL* 3.6 27.1 - - + -
586B PHE* 4.3 16.2 - - + -
588B LEU* 4.0 27.1 - - + -
598B PHE* 6.0 0.2 - - + -
609B TRP* 2.9 38.9 + - + +
610B VAL 4.1 0.2 - - - +
612B ALA* 1.3 72.2 - - - +
614B HIS* 1.3 66.1 + - + +
616B ALA* 3.2 3.9 + - + +
617B CYS* 2.9 37.5 + - - -
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Residues in contact with HIS 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B SER 4.3 3.6 - - - -
572B ILE* 3.8 1.8 - - - -
573B VAL* 2.9 52.5 + - + +
610B VAL* 3.0 26.2 + - + +
613B ILE* 1.3 78.5 - - + +
615B SER* 1.3 57.2 - - - +
617B CYS* 3.4 2.1 + - - +
618B ALA* 2.8 29.7 + - - +
694B CYS* 3.6 24.8 + - + +
695B TYR* 3.7 36.1 - + + -
698B SER* 2.9 35.4 + - - +
704B LEU* 3.8 6.3 - - + -
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Residues in contact with SER 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ARG* 3.4 23.9 + - - -
611B THR* 2.5 33.4 + - - +
612B ALA* 3.7 2.7 - - - -
614B HIS* 1.3 74.4 - - - +
616B ALA* 1.3 65.3 + - - +
618B ALA* 3.2 2.8 + - - +
619B SER* 2.9 25.3 + - - -
698B SER* 4.2 5.4 + - - -
699B LEU* 3.9 29.6 - - - +
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Residues in contact with ALA 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ARG* 3.7 21.9 - - - +
540B LEU* 4.3 9.6 - - + -
542B GLY 3.2 28.1 - - - +
543B CYS* 3.3 12.5 - - - -
612B ALA 3.0 17.4 + - - +
613B ILE* 3.6 4.9 - - + +
615B SER* 1.3 75.3 - - - +
617B CYS* 1.3 62.7 + - - +
619B SER* 3.2 4.6 + - - -
620B LEU* 3.0 19.1 + - - +
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Residues in contact with CYS 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B CYS* 3.6 11.9 - - - -
568B ALA* 3.0 31.4 - - - -
570B ASP* 3.9 8.4 + - - +
571B SER* 3.6 19.3 - - - -
613B ILE* 2.9 27.8 + - - +
614B HIS 3.6 1.3 - - - +
616B ALA* 1.3 74.9 - - - +
618B ALA* 1.3 60.2 + - - +
620B LEU* 3.3 2.2 + - - +
621B PHE* 2.8 30.8 + - - +
695B TYR* 3.4 26.6 - - + +
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Residues in contact with ALA 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B HIS 2.8 20.4 + - - +
615B SER* 3.2 6.5 + - - +
617B CYS* 1.3 73.8 - - - +
619B SER* 1.3 64.6 + - - +
621B PHE* 3.3 4.7 + - - +
622B ALA* 2.9 24.8 + - - +
630B THR* 3.6 21.6 - - + +
634B LEU* 4.3 2.5 - - + -
695B TYR* 3.7 28.4 - - + -
699B LEU* 3.9 13.7 - - + -
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Residues in contact with SER 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ARG* 4.3 13.6 + - - -
615B SER 2.9 13.6 + - - -
616B ALA* 3.3 10.1 - - - -
618B ALA* 1.3 75.8 - - - +
620B LEU* 1.3 63.6 + - - +
622B ALA* 3.3 4.5 + - - +
623B LYS* 3.2 43.4 + - - +
630B THR* 4.5 10.3 - - - +
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B CYS* 3.7 27.6 - - + +
569B GLU* 3.4 40.2 - - + +
616B ALA 3.0 16.0 + - - +
617B CYS* 3.8 2.5 - - - +
619B SER* 1.3 72.5 + - - +
621B PHE* 1.3 67.0 + - - +
623B LYS* 3.2 17.4 + - + +
624B LYS* 3.1 47.5 + - + +
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Residues in contact with PHE 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B ASP* 3.7 22.9 + - - +
617B CYS 2.8 18.5 + - - +
618B ALA* 3.3 7.6 + - - +
620B LEU* 1.3 79.4 - - - +
622B ALA* 1.3 63.4 + - + +
624B LYS* 3.4 7.4 + - + +
625B HIS* 3.1 56.4 + + - -
633B LEU* 3.9 22.2 - - + -
634B LEU* 4.1 14.8 - - + -
637B GLN* 4.0 18.8 - - + -
691B ARG* 4.3 9.0 - - - -
692B MET* 3.8 37.9 - - + -
695B TYR* 4.6 2.9 - - + -
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Residues in contact with ALA 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B ALA 2.9 16.3 + - - +
619B SER 3.6 4.5 - - - +
621B PHE* 1.3 74.7 - - - +
623B LYS* 1.3 60.2 + - + +
625B HIS* 2.9 16.5 + - - +
627B LYS* 2.9 34.5 + - - +
630B THR* 3.5 28.5 - - + +
633B LEU* 3.4 19.7 - - + -
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Residues in contact with LYS 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B SER* 3.2 28.9 + - - +
620B LEU* 3.2 20.4 + - + +
622B ALA* 1.3 76.7 - - + +
624B LYS* 1.3 61.1 + - + +
625B HIS 3.0 0.2 - - - -
626B GLY* 2.9 19.4 + - - +
627B LYS 4.5 5.6 - - - +
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Residues in contact with LYS 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLU* 2.7 39.8 + - - +
570B ASP* 5.9 0.4 - - - +
620B LEU* 3.1 34.6 + - + +
621B PHE* 3.8 8.7 - - + +
622B ALA 3.2 0.2 - - - -
623B LYS* 1.3 77.1 - - + +
625B HIS* 1.3 65.1 + - + +
626B GLY 3.3 0.8 + - - -
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Residues in contact with HIS 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 3.1 46.5 + + - -
622B ALA 2.9 9.6 + - - +
624B LYS* 1.3 83.0 - - + +
626B GLY* 1.3 63.2 + - - +
627B LYS* 3.2 18.5 + - + +
633B LEU* 3.6 26.5 - - + -
637B GLN* 3.8 22.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il